VCF
Row
Filter
|
Species
|
Number of variants (raw)
|
Number of SNPs (raw)
|
Number of indels (raw)
|
Number of MNPs (raw)
|
SNPs (after removing 5bps around indels, %)
|
Filter QD<10 (%)
|
Filter QUAL<30 (%)
|
Filter AVGGQ<20 (%)
|
Filter AVGDP<10 (%)
|
Upper depth cutoff
|
Filter AVGDPcutoff
|
Filter MQ<40 (%)
|
Filter FS<60 (%)
|
Filter SOR<3 (%)
|
Filter MQRankSum
|
Filter ReadPosRankSum
|
Number SNPs pass
|
SNPs pass (% from indel5bp)
|
SNPs pass (% from raw)
|
|
|
Aboye
|
78.708
M
|
64.269
M
|
16.31
M
|
11.651
M
|
60.3747
|
8.0715
|
0
|
11.2172
|
32.4490
|
42
|
0.6652
|
12.2994
|
0.3451
|
4.0712
|
0.0015
|
0.0002
|
28.504
M
|
59.9825
|
44.3503
|
|
Peryt
|
62.125
M
|
50.705
M
|
13.109
M
|
10.981
M
|
56.8140
|
9.6620
|
0
|
4.2660
|
10.1566
|
45
|
0.5506
|
5.8098
|
0.2458
|
2.0874
|
0.0014
|
0.0002
|
28.007
M
|
79.3502
|
55.2347
|
|
Cjuli
|
52.346
M
|
43.361
M
|
10.193
M
|
7.586
M
|
63.1596
|
8.6502
|
0
|
8.5288
|
21.1054
|
40
|
0.5890
|
8.7079
|
0.4691
|
2.7667
|
0.0007
|
0.0001
|
23.362
M
|
70.6602
|
53.8773
|
|
Dpunt
|
53.097
M
|
44.481
M
|
9.459
M
|
5.827
M
|
67.0303
|
8.0205
|
0
|
7.9463
|
15.8367
|
34
|
0.5573
|
9.8264
|
0.2480
|
3.3900
|
0.0005
|
0.0001
|
26.624
M
|
74.8044
|
59.8537
|
|
Gnige
|
54.858
M
|
43.486
M
|
13.058
M
|
11.351
M
|
51.6751
|
9.3795
|
0
|
9.7425
|
21.4863
|
48
|
1.0416
|
4.9387
|
1.7740
|
2.2622
|
0.0022
|
0.0003
|
19.423
M
|
68.5179
|
44.6659
|
|
Scabr
|
41.577
M
|
32.814
M
|
9.882
M
|
7.614
M
|
55.7784
|
7.4074
|
0
|
1.3659
|
3.4610
|
51
|
0.5945
|
1.8352
|
0.2611
|
1.0953
|
0.0022
|
0.0003
|
20.524
M
|
88.5020
|
62.5475
|
|
Spilc
|
53.509
M
|
39.236
M
|
16.384
M
|
12.063
M
|
48.1100
|
13.9271
|
0
|
13.2966
|
26.1786
|
51
|
0.5448
|
10.7754
|
0.2210
|
4.4008
|
0.0008
|
0.0003
|
15.543
M
|
60.3771
|
39.6142
|
|
Lmorm
|
29.992
M
|
24.632
M
|
5.918
M
|
3.757
M
|
67.2032
|
7.1111
|
0
|
4.0199
|
9.5812
|
55
|
0.5193
|
6.8731
|
0.4881
|
2.7649
|
0.0029
|
0.0003
|
16.482
M
|
81.7762
|
66.9149
|
|
Msurm
|
32.532
M
|
26.455
M
|
7.078
M
|
5.708
M
|
60.3445
|
7.6958
|
0
|
2.1531
|
4.6326
|
64
|
0.6013
|
3.5797
|
0.3723
|
2.0339
|
0.0030
|
0.0005
|
16.876
M
|
85.9666
|
63.7936
|
|
Cgale
|
28.08
M
|
23.266
M
|
5.481
M
|
3.644
M
|
68.5133
|
9.1767
|
0
|
9.2604
|
16.6887
|
62
|
0.7612
|
12.7323
|
0.6687
|
3.8219
|
0.0037
|
0.0007
|
14.102
M
|
73.2985
|
60.6105
|
|
Ssard
|
28.459
M
|
22.286
M
|
6.819
M
|
4.256
M
|
61.0671
|
6.6099
|
0
|
2.5047
|
6.4139
|
53
|
0.3512
|
2.7936
|
0.3158
|
1.6742
|
0.0012
|
0.0002
|
14.979
M
|
86.1882
|
67.2123
|
|
Scant
|
24.817
M
|
19.797
M
|
5.56
M
|
3.391
M
|
64.7264
|
10.4272
|
0
|
3.2330
|
6.7445
|
48
|
0.9775
|
5.4170
|
0.6916
|
2.4746
|
0.0025
|
0.0003
|
13.127
M
|
81.7206
|
66.3072
|
|
Lbude
|
22.488
M
|
18.594
M
|
4.1
M
|
1.436
M
|
73.3165
|
3.6672
|
0
|
1.2677
|
1.4681
|
62
|
0.6664
|
2.3091
|
0.2487
|
1.1356
|
0.0018
|
0.0003
|
15.419
M
|
93.5234
|
82.9260
|
|
Scine
|
21.28
M
|
16.382
M
|
5.467
M
|
3.512
M
|
59.4479
|
8.6106
|
0
|
3.8303
|
8.7132
|
71
|
0.8342
|
7.8203
|
1.0086
|
2.5603
|
0.0061
|
0.0006
|
10.209
M
|
80.7016
|
62.3201
|
|
Mmerl
|
18.857
M
|
13.227
M
|
6.437
M
|
4.433
M
|
48.7834
|
17.3570
|
0
|
7.9431
|
13.5601
|
72
|
1.3609
|
11.2877
|
1.4988
|
4.5794
|
0.0055
|
0.0009
|
6.099
M
|
66.2996
|
46.1110
|
|
Dlabr
|
13.366
M
|
10.586
M
|
3.001
M
|
1.541
M
|
67.5807
|
12.1566
|
0
|
2.5158
|
4.5965
|
49
|
1.3273
|
4.7543
|
0.5625
|
2.8535
|
0.0018
|
0.0004
|
7.427
M
|
82.2231
|
70.1604
|
|
Styph
|
14.813
M
|
11.897
M
|
3.303
M
|
2.235
M
|
62.5797
|
5.0903
|
0
|
1.0889
|
2.1179
|
118
|
0.5246
|
3.9792
|
0.7381
|
1.9171
|
0.0136
|
0.0014
|
8.425
M
|
90.8816
|
70.8123
|
|
Afall
|
15.839
M
|
10.419
M
|
5.767
M
|
2.786
M
|
51.4755
|
16.4986
|
0
|
8.7760
|
15.1129
|
62
|
0.9240
|
8.2993
|
0.9779
|
5.0038
|
0.0025
|
0.0012
|
5.491
M
|
67.3449
|
52.6973
|
|
Hgutt
|
4.176
M
|
3.008
M
|
1.254
M
|
0.6
M
|
61.1707
|
8.1805
|
0
|
2.2114
|
3.0368
|
108
|
0.2421
|
2.3358
|
1.1716
|
2.9105
|
0.0073
|
0.0009
|
2.243
M
|
87.7844
|
74.5633
|
Species
|
Species
|
Number of SNPs
|
Transitions (Ts)
|
Transversions (Tv)
|
Ts/Tv
|
|
Atherina boyeri
|
28.504
M
|
15283372
|
13220130
|
1.16
|
|
Alosa fallax
|
5.491
M
|
3074108
|
2416542
|
1.27
|
|
Coryphoblennius galerita
|
14.102
M
|
8008818
|
6092833
|
1.31
|
|
Coris julis
|
23.362
M
|
13321677
|
10039823
|
1.33
|
|
Dicentrarchus labrax
|
7.427
M
|
3989194
|
3438013
|
1.16
|
|
Diplodus puntazzo
|
26.624
M
|
16043571
|
10580196
|
1.52
|
|
Gobius niger
|
19.423
M
|
10990524
|
8432971
|
1.30
|
|
Hippocampus guttulatus
|
2.243
M
|
1272317
|
970318
|
1.31
|
|
Lophius budegassa
|
15.419
M
|
7771877
|
7647453
|
1.02
|
|
Lithognathus mormyrus
|
16.482
M
|
9505578
|
6976802
|
1.36
|
|
Merluccius merluccius
|
6.099
M
|
3692784
|
2406158
|
1.53
|
|
Mullus surmuletus
|
16.876
M
|
9734752
|
7141627
|
1.36
|
|
Pagellus erythrinus
|
28.007
M
|
16440864
|
11566160
|
1.42
|
|
Serranus cabrilla
|
20.524
M
|
11104907
|
9419531
|
1.18
|
|
Spondyliosoma cantharus
|
13.127
M
|
8249303
|
4877674
|
1.69
|
|
Symphodus cinereus
|
10.209
M
|
5921071
|
4288108
|
1.38
|
|
Sardina pilchardus
|
15.543
M
|
9119002
|
6424066
|
1.42
|
|
Sarda sarda
|
14.979
M
|
8751501
|
6227148
|
1.41
|
|
Syngnathus typhle
|
8.425
M
|
4935044
|
3489717
|
1.41
|
Phased genotype percentage